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The mosque was originally built in 1950 at Roosevelt Road in Taipei. Because of the expansion of roads a few year later, the mosque was moved to Xinhai Road. It was reopened in 1983. The mosque was inaugurated by the Ambassador of Saudi Arabia to the ROC, Assad Abdul Aziz Al-Zuhair. The mosque was renovated on April 2010 with help from the Indonesian Economic and Trade Office to Taipei.

The mosque serves as the headquarters of the Chinese Muslim Youth League. It also houses the office of the Taiwan Halal Integrity Development Association, a group that issues Halal certification to food products produced in Taiwan for Muslims to eat. The mosque also has dormitories for Muslim travelers and foreign missionaries to stay.

It is not like Taipei Grand Mosque, which is heavily supported by the ROC government and Kuomintang. Taipei Cultural Mosque depends heavily on private donations. This makes it a purely civilian mosque concentrating on religious affairs.